I would not necessarily consider the answer to be rude with respect to the phrase itself.
First of all, consider the literal interpretation of the phrase. If I'm playing poker, and I don't have a full deck, it means that I actually don't have a full deck. It doesn't mean that I'm crazy, but that I'm missing one of more cards.
Here's the response again, with my own emphasis:
Both you and your friend are incorrect; sorry. But that's not your fault; you're not playing with a full deck, if you take your definitions of "part of speech" from English books.
I take the emphasis to mean that it's not their fault either intentionally or due to the nature of them being stupid.
Just as plumber might not have all the tools required for a particular job, I interpret the passage as saying that the person and his friend don't have all the linguistic tools necessary to understand a particular meaning.
In short, not playing with a full deck is still being used metaphorically, but not metaphorically in the way that it's commonly used.
On the other hand, even if the expression isn't being used in the normal stupid sense, the answer itself could still be interpreted as somewhat conceited. It's not clear, because it's missing a tone of voice. It's possible to read it as a simple statement of fact—or to read it as a put-down.
Since it can be interpreted in an insulting fashion, even if that wasn't the intention, I think it should be edited to remove the questionable phrasing.
PS: I actually flagged the answer in question for moderator attention (calling out the second sentence), as I wasn't sure exactly how to edit it in a way that would be appropriate for everybody involved.